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MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Eva C. Sonnenschein Orcid Logo, Mitja M Zdouc, Kai Blin Orcid Logo, Nico L L Louwen, Jorge Navarro Orcid Logo, Catarina Loureiro Orcid Logo, Chantal D Bader, Constance B Bailey, Lena Barra, Thomas J Booth, Kenan A J Bozhüyük, José D D Cediel-Becerra, Zachary Charlop-Powers, Marc G Chevrette, Yit Heng Chooi, Paul M D’Agostino, Tristan de Rond, Elena Del Pup, Katherine R Duncan, Wenjia Gu, Novriyandi Hanif, Eric J N Helfrich, Matthew Jenner, Yohei Katsuyama, Aleksandra Korenskaia, Daniel Krug, Vincent Libis, George A Lund, Shrikant Mantri, Kalindi D Morgan, Charlotte Owen, Chin-Soon Phan, Benjamin Philmus, Zachary L Reitz, Serina L Robinson, Kumar Saurabh Singh, Robin Teufel, Yaojun Tong, Fidele Tugizimana, Dana Ulanova, Jaclyn M Winter, César Aguilar, Daniel Y Akiyama, Suhad A A Al-Salihi, Mohammad Alanjary, Fabrizio Alberti, Gajender Aleti, Shumukh A Alharthi, Mariela Y Arias Rojo, Amr A Arishi, Hannah E Augustijn, Nicole E Avalon, J Abraham Avelar-Rivas, Kyle K Axt, Hellen B Barbieri, Julio Cesar J Barbosa, Lucas Gabriel Barboza Segato, Susanna E Barrett, Martin Baunach, Christine Beemelmanns, Dardan Beqaj, Tim Berger, Jordan Bernaldo-Agüero, Sandra M Bettenbühl, Vincent A Bielinski, Friederike Biermann, Ricardo M Borges, Rainer Borriss, Milena Breitenbach, Kevin M Bretscher, Michael W Brigham, Larissa Buedenbender, Brodie W Bulcock, Carolina Cano-Prieto, João Capela, Victor J Carrion, Riley S Carter, Raquel Castelo-Branco, Gabriel Castro-Falcón, Fernanda O Chagas, Esteban Charria-Girón, Ayesha Ahmed Chaudhri, Vasvi Chaudhry, Hyukjae Choi, Yukyung Choi, Roya Choupannejad, Jakub Chromy, Melinda S Chue Donahey Orcid Logo, Jérôme Collemare, Jack A Connolly, Kaitlin E Creamer, Max Crüsemann, Andres Arredondo Cruz, Andres Cumsille, Jean-Felix Dallery, Luis Caleb Damas-Ramos, Tito Damiani, Martinus de Kruijff, Belén Delgado Martín, Gerardo Della Sala, Jelle Dillen, Drew T Doering, Shravan R Dommaraju, Suhan Durusu, Susan Egbert, Mark Ellerhorst, Baptiste Faussurier, Artem Fetter, Marc Feuermann, David P Fewer, Jonathan Foldi, Andri Frediansyah, Erin A Garza, Athina Gavriilidou, Andrea Gentile, Jennifer Gerke, Hans Gerstmans, Juan Pablo Gomez-Escribano, Luz A González-Salazar, Natalie E Grayson, Claudio Greco, Juan E Gris Gomez, Sebastian Guerra, Shaday Guerrero Flores, Alexey Gurevich, Karina Gutiérrez-García, Lauren Hart, Kristina Haslinger, Beibei He, Teo Hebra, Jethro L Hemmann, Hindra Hindra, Lars Höing, Darren C Holland, Jonathan E Holme, Therese Horch, Pavlo Hrab, Jie Hu, Thanh-Hau Huynh, Ji-Yeon Hwang, Riccardo Iacovelli, Dumitrita Iftime, Marianna Iorio, Sidharth Jayachandran, Eunah Jeong, Jiayi Jing, Jung J Jung, Yuya Kakumu, Edward Kalkreuter, Kyo Bin Kang, Sangwook Kang, Wonyong Kim, Geum Jin Kim, Hyunwoo Kim, Hyun Uk Kim, Martin Klapper, Robert A Koetsier, Cassandra Kollten, Ákos T Kovács, Yelyzaveta Kriukova, Noel Kubach, Aditya M Kunjapur, Aleksandra K Kushnareva, Andreja Kust, Jessica Lamber, Martin Larralde, Niels J Larsen, Adrien P Launay, Ngoc-Thao-Hien Le, Sarah Lebeer, Byung Tae Lee, Kyungha Lee, Katherine L Lev, Shu-Ming Li, Yong-Xin Li, Cuauhtémoc Licona-Cassani, Annette Lien, Jing Liu, Julius Adam V Lopez, Nataliia V Machushynets, Marla I Macias, Taifo Mahmud, Matiss Maleckis, Añadir Maharai Martinez-Martinez, Yvonne Mast, Marina F Maximo, Christina M McBride, Rose M McLellan, Khyati Mehta Bhatt, Chrats Melkonian, Aske Merrild, Mikko Metsä-Ketelä, Douglas A Mitchell, Alison V Müller, Giang-Son Nguyen, Hera T Nguyen, Timo H J Niedermeyer, Julia H O’Hare, Adam Ossowicki, Bohdan O Ostash, Hiroshi Otani, Leo Padva, Sunaina Paliyal, Xinya Pan, Mohit Panghal, Dana S Parade, Jiyoon Park, Jonathan Parra, Marcos Pedraza Rubio, Huong T Pham, Sacha J Pidot, Jörn Piel, Bita Pourmohsenin, Malik Rakhmanov, Sangeetha Ramesh, Michelle H Rasmussen, Adriana Rego, Raphael Reher, Andrew J Rice, Augustin Rigolet, Adriana Romero-Otero, Luis Rodrigo Rosas-Becerra, Pablo Y Rosiles, Adriano Rutz, Byeol Ryu, Libby-Ann Sahadeo, Murrel Saldanha, Luca Salvi, Eduardo Sánchez-Carvajal, Christian Santos-Medellin, Nicolau Sbaraini, Sydney M Schoellhorn, Clemens Schumm, Ludek Sehnal, Nelly Selem, Anjali D Shah, Tania K Shishido, Simon Sieber, Velina Silviani, Garima Singh, Hemant Singh, Nika Sokolova, Eva C Sonnenschein, Margherita Sosio, Sven T Sowa, Karin Steffen, Evi Stegmann, Alena B Streiff, Alena Strüder, Frank Surup, Tiziana Svenningsen, Douglas Sweeney, Judit Szenei, Azat Tagirdzhanov, Bin Tan, Matthew J Tarnowski, Barbara R Terlouw, Thomas Rey, Nicola U Thome, Laura Rosina Torres Ortega, Thomas Tørring, Marla Trindade, Andrew W Truman, Marie Tvilum, Daniel W Udwary, Christoph Ulbricht, Lisa Vader, Gilles P van Wezel, Max Walmsley, Randika Warnasinghe, Heiner G Weddeling, Angus N M Weir, Katherine Williams, Sam E Williams, Thomas E Witte, Steffaney M Wood Rocca, Keith Yamada, Dong Yang, Dongsoo Yang, Jingwei Yu, Zhenyi Zhou, Nadine Ziemert, Lukas Zimmer, Alina Zimmermann, Christian Zimmermann, Justin J J van der Hooft Orcid Logo, Roger G Linington Orcid Logo, Tilmann Weber Orcid Logo, Marnix H Medema Orcid Logo, Shumukh Alharthi, Claudio Greco Orcid Logo

Nucleic Acids Research, Volume: 53, Issue: D1, Pages: D678 - D690

Swansea University Authors: Eva C. Sonnenschein Orcid Logo, Shumukh Alharthi, Claudio Greco Orcid Logo

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DOI (Published version): 10.1093/nar/gkae1115

Abstract

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes...

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Published in: Nucleic Acids Research
ISSN: 0305-1048 1362-4962
Published: Oxford University Press (OUP) 2025
Online Access: Check full text

URI: https://cronfa.swan.ac.uk/Record/cronfa68571
Abstract: Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
College: Faculty of Science and Engineering
Funders: M.M.Z. was supported by the NWO Grant KICH1.LWV04.21.013 and by the Horizon 2020 Grant 101000392; C.L. was supported by the NWO Open Science Project 'BiG-CODEC' No. OSF.23.1.044; C.D.B was supported by the German Research Foundation Grant No. 547394769; C.B.B. was supported by the University of Sydney Drug Discovery Initiative; T.J.B was supported by the Novo Nodisk Foundation Grant NNF22OC0078997; Y.H.C. was supported by the Australian Research Council Industry Fellowship IM230100154; P.M.D. was supported by the Hans Fischer Society; K.R.D. was supported by the UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate and by the United Kingdom Research and Innovation (EP/X03142X/1) and by the Horizon Europe Marie Skłodowska-Curie grant agreement No 101072485; N.H. was supported by the Indonesia Endowment Fund for Education Agency (LPDP) and National Research and Innovation Agency (BRIN) of the Republic of Indonesia (106/IV/KS/11/2023 and 41644/IT3/PT.01.03/P/B/2023) and by the the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia (027/E5/PG.02.00.PL/2024); M.J. was supported by the UKRI Future Leaders Fellowship (MR/W011247/1); A.Korenskaia was supported by the Horizon Europe Marie Skłodowska-Curie grant agreement No 101072485; V.L. was supported by the ERC Starting Grant 101117891-MeDiSyn and by the Agence Nationale de la Recherche project ANR-22-CE44-0011-01 UMISYN; G.A.L. was supported by the Growing Health Institute Strategic Programme (BB/X010953/1; BBS/E/RH/230003B); S.M. was supported by the Department of Biotechnology (DBT), Government of India and by the National Agri-Food Biotechnology Institute (NABI); C-S.P. was supported by the EU project No. 101087181 (Natural Products Research at Latvian Institute of Organic Synthesis as a Driver for Excellence in Innovation); R.T. was supported by the Swiss National Science Foundation (SNSF), grant 212747; Y.T. was supported by the National Key Research and Development Program of China (2021YFA0909500) and by the the National Natural Science Foundation of China (32170080 and 32370026) and by the Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University; D.U. was supported by the Japan Society for Promotion of Science KAKENHI grant number 21K06336; D.Y.A. was supported by the São Paulo Research Foundation (FAPESP) research scholarship (grant 21/07038-0); M.A. was supported by the NWO Talent programme Veni science domain (VI.Veni.202.130); F.A. was supported by the UKRI Future Leaders Fellowship (MR/V022334/1); G.A. was supported by the USDA Evans-Allen Research Grant (222676); N.E.A. was supported by the National Center for Complementary and Integrative Health of the NIH under award number F32AT011475; H.B.B. was supported by the São Paulo Research Foundation (FAPESP) research scholarship (grant 21/08947-3); S.E.B. was supported by the National Science Foundation Graduate Research Fellowship (DGE 21-46756) and by the the University of Illinois Urbana-Champaign Illinois Distinguished Fellowship; C.B. was supported by the European Union Horizon 2020 research and innovation program (ERC Grant number: 802736, MORPHEUS); J.B-A. was supported by the Consejo Nacional de Ciencia y Tecnología (CONACyT) [735867]; K.M.B. was supported by the NWO Merian fund (Micro-GRICE); M.W.B. was supported by the United Kingdom Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) funded White Rose Mechanistic and Structural Biology Doctoral Training Program (BB/T007222/1); L.B. was supported by the Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship funded by the European Union (Project chelOMICS - grant agreement No. 101066127); V.J.C. was supported by the Ministerio de Ciencia, Innovación y Universidades project RYC2020-029240-I; R.C-B. was supported by the scholarship SFRH/BD/136367/2018 by Fundaçao para a Ciencia e Tecnologia (FCT); G.C-F. was supported by the National Institutes of Health (NIH)/NIGMS K12 GM068524 Award as a San Diego IRACDA Scholar.; E.C-G. was supported by the HZI POF IV Cooperativity and Creativity Project Call; V.C. was supported by the Alexander von Humboldt-Stiftung (Ref: 3.5-IND-1199743-HFST-P) and by the Cluster of Excellence: Controlling Microbes to Fight Infection (CMFI-YIG (EXC-2124/1-09.029_0; H.C. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1A6A1A03044512, and NRF-2021R1A2C1010727); Y.C. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1C1C1004046 and NRF-2022R1A5A2021216); J.A.C. was supported by the Signals in the Soil program via UK Research and Innovation (UKRI; NE/T010959/1); K.E.C. was supported by the Chan Zuckerberg Initiative Foundation grant number CZIF2022-007203; M.C. was supported by the German Research Foundation (DFG) Grant No. 495740318; J-F.D. was supported by the Agence Nationale de la Recherche (ShySM grant ANR-24-CE20-7299-01 and by the EUR Saclay Plant Sciences-SPS (ANR-17-EUR-0007); L.C.D-R. was supported by the European Union's Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No 101072485 (MAGic-MOLFUN); T.D. was supported by the European Regional Development Fund, Programme Johannes Amos Comenius project ‘IOCB MSCA PF Mobility’ no. CZ.02.01.01/00/22_010/0002733; M.dK. was supported by the European Union's Horizon 2020 research and innovation program (ERC Grant number: 802736, MORPHEUS).; A.Fetter was supported by the United Kingdom Research and Innovation (EP/X03142X/1) and by the Horizon Europe Marie Skłodowska-Curie grant agreement No 101072485; M.F. was supported by the Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI; A.Frediansyah was supported by the Fulbright Grant (PS00349981); A.Gavriilidou was supported by the Deutsche Forschungsgemeinschaft [398967434-TRR 261]; A.Gentile was supported by the Italian Ministry of Research (Grant DM60066); H.G. was supported by the Research Foundation–Flanders (FWO) under the scope of junior postdoctoral fellowship (1229222N); L.A.G-S. was supported by the CONAHCYT scholarship (#971765); N.E.G. was supported by the NIGMS R01-GM146224, NERRS NA22NOS4200050; C.G. was supported by the BBSRC (BB/V005723/2); J.E.G.G. was supported by the CONAHCYT scholarship (#1347411); S.G. was supported by the National Institutes of Health (NIH), Grant T32GM136583. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.; L.H. was supported by the NIH F31 1F31ES036421-01; T.Hebra was supported by the European Union's Horizon Europe research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101130799; T.Horch was supported by the Novo Nordisk Foundation grant-number: CFB 2.0, NNF20CC0035580; M.I. was supported by the Italian Ministry of Research (Grant DM60066); E.J. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1C1C1004046 and NRF-2022R1A5A2021216); K.B.K. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1C1C1004046 and NRF-2022R1A5A2021216); S.K. was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-RS-2024-00408499) and by the National Research Foundation of Korea grants funded by the Republic of Korean Government (Ministry of Science and ICT) (NRF-RS-2024-00352229); W.K. was supported by the National Research Foundation of Korea grant funded by the Korea government (No. 2022R1C1C2004118); G.J.K. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1A6A1A03044512, and NRF-2021R1A2C1010727); H.K. was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea Government (MSIT) Grants NRF 2018R1A5A2023127 and RS-2023-00211868; M.K. was supported by the Werner Siemens Foundation grant Paleobiotechnology; R.A.K. was supported by the NWO-XL (OCENW.XL21.XL21.088); A.T.K. was supported by the Danish National Research Foundation CeMiSt, DNRF137 and by the Novo Nordisk Foundation INTERACT, NNF19SA0059360; A.M.K. was supported by the U.S. National Science Foundation (CBET-2032243); A.Kust was supported by the Delta Stewardship Council Delta Science Program; S.L. was supported by the European Research Council under European Union's Horizon 2020 Research and Innovation Program ERC St grant 852600 Lacto-Be; S-M.L. was supported by the Deutsche Forschungsgemeinschaft LI844/11-1 and LI844/14-1; A.L. was supported by the European Union's Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No 101072485 (MAGic-MOLFUN); M.I.M. was supported by the Conahcyt Mexico International PhD Studentship and by the Strathclyde University Global Research Scholarship; M.M. was supported by the Novo Nordisk Foundation (Grant NNF23OC0082881) and Innovation Fund Denmark (Grant 3141-00013A); Y.M. was supported by the Leibniz Association grant K445/2022; M.F.M. was supported by the São Paulo Research Foundation (FAPESP) research scholarship (grant 23/01956-2); C.M.M. was supported by the NSF GRFP (#DGE 2241144); C.M. was supported by the MiCRop Consortium (NWO/OCW grant no. 024.004.014); A.M. was supported by the Carlsberg Foundation (CF22-1239); G-S.N. was supported by the SINTEF internal projects, POP-SEP BiocatDB (102022750), SEP AGREE (102029187) and POS BIOINFO 2024 (102024676-14), European Union's Horizon 2020 research and innovation programme under Grant Agreement no. 101000392 (MARBLES), no. 101081957 (BLUETOOLS), and no. 862923 (AtlantECO); A.O. was supported by the Marie Sklodowska-Curie grant No. 101106349; B.O.O. was supported by the BG-21F, Ministry of Education and Science of Ukraine and by the 57/0009, National Research Fund of Ukraine (partial support); H.O. was supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231; L.P. was supported by the German Academic Scholarship Foundation; X.P. was supported by the NWO-XL grant OCENW.GROOT.2019.063; M.P. was supported by the Department of Biotechnology (DBT), Government of India and by the University Grants Commission (UGC), Ministry of Education, Government of India; M.P.R. was supported by the Spanish “Junta de Andalucía” project PROYEXCEL_00012; H.T.P. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1C1C1004046 and NRF-2022R1A5A2021216); S.J.P. was supported by the National Health and Medical Research Council GNT2021638, Australian Research Council Discovery Project DP230102668; B.P. was supported by the SECRETed EU Project Horizon 2020 (101000794); M.H.R. was supported by the European Research Council (ERC), European Union's Horizon 2020 Research and Innovation Program (grant agreement no. 865738); A.J.R. was supported by the Chemical-Biology Interface Training Grant (Grant T32-GM136629) and a National Science Foundation Graduate Research Fellowship (Grant DGE 21-46756); A.R. was supported by the ERC Advanced Grant 101055020-COMMUNITY; L.R.R-B. was supported by the Consejo Nacional de Ciencia y Tecnología (CONACyT) [757173]; L.Salvi was supported by the European Union's Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No 101072485 (MAGic-MOLFUN); E.S-C. was supported by the PhD scholarships ANID N° 21231991; L.Sehnal was supported by the Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship funded by the European Union (Project NAfrAM - grant agreement No. 10106428); A.D.S. was supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership [BB/T008741/1]; T.K.S. was supported by the Novo Nordisk Foundation (Grant number: NNF22OC0080109); V.S. was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIT) (Grant No. NRF-2020R1A6A1A03044512, and NRF-2021R1A2C1010727); E.C.S. was supported by the Pathfinder Open 2022, a European Innovation Council (EIC) work programme that is part of Horizon Europe (grant agreement no. 101099528) and UK Innovation Funding Agency (UKRI) (reference no. 10062709).; M.S. was supported by the Italian Ministry of Research (Grant DM60066); K.S. was supported by the Swedish Pharmaceutical Society PostDoc stipend; A.B.S. was supported by the Swiss National Science Foundation (SNSF, 205320_219638); T.S. was supported by the Carlsberg Foundation (CF22-1239); J.S. was supported by the European Union's Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No 101072485 (MAGic-MOLFUN); A.T. was supported by the Saarland University through the NextAID project; M.J.T. was supported by the Pathfinder Open 2022, a European Innovation Council (EIC) work programme that is part of Horizon Europe (grant agreement no. 101099528) and UK Innovation Funding Agency (UKRI) (reference no. 10062709).; T.T. was supported by the Carlsberg Foundation (CF22-1239); A.W.T. was supported by the BBSRC Institute Strategic Program grant (BB/X01097X/1); M.T. was supported by the AUFF (AUFF-E-2022-9-42); L.V. was supported by the European Union's Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No 101072485 (MAGic-MOLFUN); G.P.vW. was supported by the ERC Advanced Grant 101055020-COMMUNITY; K.W. was supported by the MR/N029909/1, Medical Research Council, UK; S.E.W. was supported by the Novo Nordisk Foundation Postdoctoral Fellowship (NNF22OC0079021); T.E.W. was supported by the Natural Science and Research Council of Canada PGS-D scholarship; D.Y. was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (Grant RS-2024-00440975); A.Z. was supported by the German Center for Infection Research (DZIF) (TTU 09.826); C.Z. was supported by the Austrian Science Fund (FWF) [10.55776/P 34036]; R.G.L. was supported by the Natural Sciences and Engineering Research Council of Canada Discovery Grant program; T.W. was supported by the Novo Nordisk Foundation, NNF20CC0035580 and by the Danish National Research Foundation CeMiSt, DNRF137 and by the European Union's Horizon Europe programme under the Marie Skłodowska-Curie grant agreement No 101072485 (MAGic-MOLFUN).
Issue: D1
Start Page: D678
End Page: D690

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